Conformational fluctuations and rotational tumbling of proteins can be experimentally accessed with nuclear spin relaxation experiments. However, interpretation of molecular dynamics from the experimental data is often complicated, especially for molecules with anisotropic shape. Here, we apply classical molecular dynamics simulations to interpret the conformational fluctuations and rotational tumbling of proteins with arbitrarily anisotropic shape. The direct calculation of spin relaxation times from simulation data did not reproduce the experimental data. This was successfully corrected by scaling the overall rotational diffusion coefficients around the protein inertia axes with a constant factor. The achieved good agreement with experiments allowed the interpretation of the internal and overall dynamics of proteins with significantly anisotropic shape. The overall rotational diffusion was found to be Brownian, having only a short subdiffusive region below 0.12 ns. The presented methodology can be applied to interpret rotational dynamics and conformation fluctuations of proteins with arbitrary anisotropic shape. However, a water model with more realistic dynamical properties is probably required for intrinsically disordered proteins.

• MeSH
• bakteriální proteiny chemie   metabolismus   MeSH
• Helicobacter pylori metabolismus   MeSH
• izotopy dusíku chemie   MeSH
• membránové proteiny chemie   metabolismus   MeSH
• proteinové domény MeSH
• simulace molekulární dynamiky * MeSH
• spinové značení MeSH
• vnitřně neuspořádané proteiny chemie   metabolismus   MeSH
• voda chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• bakteriální proteiny MeSH
• izotopy dusíku MeSH
• membránové proteiny MeSH
• Nitrogen-15 MeSH Prohlížeč
• spinové značení MeSH
• tonB protein, Bacteria MeSH Prohlížeč
• vnitřně neuspořádané proteiny MeSH
• voda MeSH